Hello
I am tring to unwarp a double dti acquisition (AP and PA). If I extract
the B0 and do the topup comand it works very well. I does a correction
which is much better than the one with a fieldmap.
I then try to run eddy on the combine data set. I merged the AP and PA
acquisition in one 4D nifti and run the eddy command
eddy --imain=4D_dti.nii.gz --mask=bmask_mask.nii.gz --index=index.txt
--acqp=acqp.txt --bvecs=bvecs --bvals=bvals --out=test
--session=session.txt
The output from eddy was a 4D volume almost identical the the input (it
did not correct for the big AP PA distorsion). May be I need to call it
with the --topup.
But it is not clear to me on which data I should run topup before eddy :
only on the B0 or on the all data set (including the direction)
Thanks for your help
Romain
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